{
    "title": "Invocation manifest for fMRIPREP: A Robust Preprocessing Pipeline for fMRI Data",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "properties": {
        "config": {
            "type": "object",
            "properties": {
                "skip-bids-validation": {
                    "type": "boolean",
                    "default": true
                },
                "task-id": {
                    "type": "string",
                    "default": ""
                },
                "echo-idx": {
                    "type": "string",
                    "default": ""
                },
                "anat-only": {
                    "type": "boolean",
                    "default": false
                },
                "error-on-aroma-warnings": {
                    "type": "boolean",
                    "default": false
                },
                "ignore": {
                    "type": "string",
                    "enum": [
                        "",
                        "fieldmaps",
                        "slicetiming",
                        "sbref"
                    ],
                    "default": ""
                },
                "longitudinal": {
                    "type": "boolean",
                    "default": false
                },
                "t2s-coreg": {
                    "type": "boolean",
                    "default": false
                },
                "bold2t1w-dof": {
                    "type": "integer",
                    "enum": [
                        6,
                        9,
                        12
                    ],
                    "default": 6
                },
                "output-spaces": {
                    "type": "string",
                    "default": "MNI152NLin2009cAsym",
                    "enum": [
                        "OASIS30ANTs",
                        "NKI",
                        "MNI152NLin2009cAsym"
                    ]
                },
                "force-bbr": {
                    "type": "boolean",
                    "default": false
                },
                "force-no-bbr": {
                    "type": "boolean",
                    "default": false
                },
                "medial-surface-nan": {
                    "type": "boolean",
                    "default": false
                },
                "dummy-scans": {
                    "type": "integer",
                    "default": 0
                },
                "use-aroma": {
                    "type": "boolean",
                    "default": false
                },
                "aroma-melodic-dimensionality": {
                    "type": "integer",
                    "default": 200
                },
                "return-all-components": {
                    "type": "boolean",
                    "default": false
                },
                "fd-spike-threshold": {
                    "type": "number",
                    "default": 2
                },
                "dvars-spike-threshold": {
                    "type": "number",
                    "default": 2
                },
                "skull-strip-fixed-seed": {
                    "type": "boolean",
                    "default": false
                },
                "skull-strip-template": {
                    "type": "string",
                    "enum": [
                        "",
                        "OASIS30ANTs",
                        "NKI"
                    ],
                    "default": "OASIS30ANTs"
                },
                "fmap-bspline": {
                    "type": "boolean",
                    "default": false
                },
                "fmap-no-demean": {
                    "type": "boolean",
                    "default": true
                },
                "use-syn-sdc": {
                    "type": "boolean",
                    "default": false
                },
                "force-syn": {
                    "type": "boolean",
                    "default": false
                },
                "no-submm-recon": {
                    "type": "boolean",
                    "default": false
                },
                "cifti-output": {
                    "type": "boolean",
                    "default": false
                },
                "fs-no-reconall": {
                    "type": "boolean",
                    "default": false
                },
                "no-track": {
                    "type": "boolean",
                    "default": false
                },
                "save-outputs": {
                    "type": "boolean",
                    "default": false
                },
                "save-intermediate-work": {
                    "type": "boolean",
                    "default": false
                },
                "intermediate-files": {
                    "default": "",
                    "type": "string"
                },
                "intermediate-folders": {
                    "default": "",
                    "type": "string"
                },
                "FREESURFER-LICENSE": {
                    "type": "string"
                },
                "reports-only": {
                    "type": "boolean",
                    "default": false
                },
                "write-graph": {
                    "type": "boolean",
                    "default": true
                },
                "sloppy": {
                    "type": "boolean",
                    "default": false
                },
                "gear-log-level": {
                    "default": "INFO",
                    "type": "string",
                    "enum": [
                        "ERROR",
                        "WARNING",
                        "INFO",
                        "DEBUG"
                    ]
                },
                "gear-dry-run": {
                    "default": false,
                    "type": "boolean"
                },
                "gear-run-bids-validation": {
                    "default": false,
                    "type": "boolean"
                }
            },
            "required": [
                "skip-bids-validation",
                "task-id",
                "echo-idx",
                "anat-only",
                "error-on-aroma-warnings",
                "ignore",
                "longitudinal",
                "t2s-coreg",
                "bold2t1w-dof",
                "output-spaces",
                "force-bbr",
                "force-no-bbr",
                "medial-surface-nan",
                "dummy-scans",
                "use-aroma",
                "aroma-melodic-dimensionality",
                "return-all-components",
                "fd-spike-threshold",
                "dvars-spike-threshold",
                "skull-strip-fixed-seed",
                "skull-strip-template",
                "fmap-bspline",
                "fmap-no-demean",
                "use-syn-sdc",
                "force-syn",
                "no-submm-recon",
                "cifti-output",
                "fs-no-reconall",
                "no-track",
                "save-outputs",
                "save-intermediate-work",
                "intermediate-files",
                "intermediate-folders",
                "reports-only",
                "write-graph",
                "sloppy",
                "gear-log-level",
                "gear-dry-run",
                "gear-run-bids-validation"
            ]
        },
        "inputs": {
            "type": "object",
            "properties": {
                "api_key": {
                    "type": "object"
                },
                "t1w-anatomy": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti"
                            ]
                        }
                    }
                },
                "t2w-anatomy": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti"
                            ]
                        }
                    }
                },
                "freesurfer-license": {
                    "type": "object",
                    "properties": {}
                }
            },
            "required": [
                "api_key"
            ]
        }
    },
    "required": [
        "config",
        "inputs"
    ]
}